mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
a4943a9e57
* add new module samtools_depth * fixed main.nf for samtools/depth * add new module mtnucratio * fix main.nf * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * layout in main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
54 lines
1.7 KiB
YAML
54 lines
1.7 KiB
YAML
name: mtnucratio
|
|
description: A small Java tool to calculate ratios between MT and nuclear sequencing reads in a given BAM file.
|
|
keywords:
|
|
- mtnucratio
|
|
- ratio
|
|
- reads
|
|
- bam
|
|
- mitochondrial to nuclear ratio
|
|
- mitochondria
|
|
- statistics
|
|
tools:
|
|
- mtnucratio:
|
|
description: A small tool to determine MT to Nuclear ratios for NGS data.
|
|
homepage: https://github.com/apeltzer/MTNucRatioCalculator
|
|
documentation: https://github.com/apeltzer/MTNucRatioCalculator
|
|
tool_dev_url: https://github.com/apeltzer/MTNucRatioCalculator
|
|
doi: "10.1186/s13059-016-0918-z"
|
|
licence: ['GPL v3']
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bam:
|
|
type: file
|
|
description: (coordinate) sorted BAM/SAM file
|
|
pattern: "*.{bam,sam}"
|
|
- mt_id:
|
|
type: string
|
|
description: Identifier of the contig/chromosome of interest (e.g. chromosome, contig) as in the aligned against reference FASTA file, e.g. mt or chrMT for mitochondria
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- mtnucratio:
|
|
type: file
|
|
description: Text file containing metrics (mtreads, mt_cov_avg, nucreads, nuc_cov_avg, mt_nuc_ratio)
|
|
pattern: "*.mtnucratio"
|
|
- json:
|
|
type: file
|
|
description: JSON file, containing metadata map with sample name, tool name and version, and metrics as in txt file
|
|
pattern: "*.json"
|
|
|
|
authors:
|
|
- "@louperelo"
|